Biomedical subjects

M Vieth

Publications and source records attributed to M Vieth.

31 records · Page 2Linked to original sources

PubMed1998

Do active site conformations of small ligands correspond to low free-energy solution structures?

We compare the low free energy structures of ten small, polar ligands in solution to their conformations in their respective receptor active sites. The solution conformations are generated by a systematic search and the free energies of representative structures are computed with a continuum solvation model. Based on the values of torsion angles, we find little similarity between low energy solution structures of small ligands and their active site conformations. However, in nine out of ten cases, the positions of 'anchor points' (key atoms responsible for tight binding) in the lowest energy solution structures are very similar to the positions of these atoms in the active site conformations. A metric that more closely captures the essentials of binding supports the basic premise underlying pharmacophore mapping, namely that active site conformations of small flexible ligands correspond to their low energy structures in solution. This work supports the efforts of building pharmacophore models based on the information present in solution structures of small isolated ligands.

Binding Sites↗

PubMed1997

Dramatic increase of alpha-hydroxyaldehydes derived from plasmalogens in the aged human brain.

Plasmalogens-substantial compounds of brain tissue--suffer degradation either by hydrolysis under production of aldehydes or by oxidation with lipid peroxylradicals by generation of plasmalogen epoxides. The latter react by addition of pentafluorobenzylhydroxylamine HCl (PFBHA HCL) under hydrolysis to alpha-hydroxyaldehydes which are immediately transformed to pentafluorobenzyloximes (PFBO). Likewise, free aldehydes are transformed to PFBO-derivatives. PFBO-derivatives of free aldehydes and PFBO-derivatives of alpha-hydroxyaldehydes were extracted and after trimethylsilylation quantified by GC/FID and by GC/MSD. The remaining aqueous phase, containing plasmalogens besides other lipids, was hydrolyzed by treatment with acid. The hydrolysis products of plasmalogens, long chain aldehydes, react with PFBHA HCl to produce PFBO-derivatives. These were also quantified by GC/FID. This method allows the quantification of plasmalogens, free aldehydes and plasmalogenepoxides in human brain samples to study changes in the relation of these compounds with increasing age. While the ratio of plasmalogens in respect to derived aldehydes seems to remain constant during life time, the quotient of plasmalogenepoxides to plasmalogens increases with age, indicating that lipid peroxidation processes are involved in the damage of plasmalogens in the brain of aged individuals, starting at an age of about 70 years.

Adolescent↗

PubMed1997

[The status of diagnosis of Barrett esophagus. An analysis of 1000 histologically diagnosed cases].

OBJECTIVE: To evaluate the quality of diagnosis in cases of Barrett's oesophagus (BOe). It was examined whether: (1) there had been regular pre-treatment investigations;(2) characteristic mucosal changes had been recognized by endoscopy; (3) a diagnosis of intraepithelial neoplasia had been made more often than of advanced Barrett carcinoma. PATIENTS AND METHODS: Endoscopic and associated bioptic reports on 1000 consecutive patients with histologically confirmed BOe, seen between 1990 and 1995, were analysed. (Average age was 63 +/- 14.3 years; male to female ratio: 2.2:1). RESULTS: In 85.1% of patients the histological diagnosis was BOe without dysplasia. The neoplasias consisted of carcinoma in 8.8%, suspected carcinoma in 0.5%, actual or suspected low-grade dysplasia in 4.6%, actual or high-grade dysplasia in 1.0%. Endoscopic diagnosis in cases without neoplasia was in 60.8% correct for actual BOe or suspected BOe. At endoscopy dysplasia was suspected in 5.4%. The diagnosis or suspected diagnosis of Barrett's carcinoma was correct in 69%. Repeat endoscopy a year after the initial diagnosis was performed in 9.4% with BOe and no neoplasia. Repeat endoscopy was performed in 37.5% of patients with an initial diagnosis of suspected low-grade dysplasia, in 43.3% with low-grade dysplasia, in 42.9% of suspected high-grade and in 100% of actual high-grade dysplasia. CONCLUSION: Neoplasia in Barrett's oesophagus is found too late. Only half of the histologically confirmed cases are found by endoscopy and follow-up is not sufficient.

Aged↗

PubMed1996

Method for predicting the state of association of discretized protein models. Application to leucine zippers.

A method that employs a transfer matrix treatment combined with Monte Carlo sampling has been used to calculate the configurational free energies of folded and unfolded states of lattice models of proteins. The method is successfully applied to study the monomer-dimer equilibria in various coiled coils. For the short coiled coils, GCN4 leucine zipper, and its fragments, Fos and Jun, very good agreement is found with experiment. Experimentally, some subdomains of the GCN4 leucine zipper form stable dimeric structures, suggesting the regions of differential stability in the parent structure. Our calculations suggest that the stabilities of the subdomains are in general different from the values expected simply from the stability of the corresponding fragment in the wild type molecule. Furthermore, parts of the fragments structurally rearrange in some regions with respect to their corresponding wild type positions. Our results suggest for an Asn in the dimerization interface at least a pair of hydrophobic interacting helical turns at each side is required to stabilize the stable coiled coil. Finally, the specificity of heterodimer formation in the Fos-Jun system comes from the relative instability of Fos homodimers, resulting from unfavorable intra- and interhelical interactions in the interfacial coiled coil region.

Amino Acid Sequence↗

PubMed1996

Predicting leucine zipper structures from sequence.

The leucine zipper structure is adopted by one family of the coiled coil proteins. Leucine zippers have a characteristic leucine repeat: Leu-X6-Leu-X6-Leu-X6-Liu (where X may be any residue). However, many sequences have the leucine repeat, but do not adopt the leucine zipper structure (we shall refer to these as non-zippers). We have found and analyzed residue pair patterns that allow one to identify correctly 90% of leucine zippers and 97% of non-zippers. Simpler analyses, based on the frequency of occurrence of residues at certain positions, specify, at most, 65% of zippers and 80-90% of non-zippers. Both short and long patterns contribute to the successful discrimination of leucine zippers from non-zippers. A number of these patterns involve hydrophobic residues that would be placed on the solvent-exposed surface of the helix, were the sequence to adopt a leucine zipper structure. Thus, an analysis of protein sequences has allowed us to improve discrimination between leucine zippers and non-zippers, and has provided some further insight into the physical factors influencing the leucine zipper structure.

Amino Acid Sequence↗

PubMed1996

Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.

A methodology for predicting coiled coil quaternary structure and for the dissection of the interactions responsible for the global fold is described. Application is made to the equilibrium between different oligomeric species of the wild type GCN4 leucine zipper and seven of its mutants that were studied by Harbury et al. Over the entire experimental concentration range, agreement with experiment is found in five cases, while in two other cases, agreement is found over a portion of the concentration range. These simulations suggest that the degree of chain association is determined by the balance between specific side chain packing preferences and the entropy reduction associated with side chain burial in higher order multimers.

Amino Acid Substitution↗

PubMed1995

Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper.

Using a simplified protein model, the equilibrium between different oligomeric species of the wild-type GCN4 leucine zipper and seven of its mutants have been predicted. Over the entire experimental concentration range, agreement with experiment is found in five cases, while in two cases agreement is found over a portion of the concentration range. These studies demonstrate a methodology for predicting coiled coil quaternary structure and allow for the dissection of the interactions responsible for the global fold. In agreement with the conclusion of Harbury et al., the results of the simulations indicate that the pattern of hydrophobic and hydrophilic residues alone is insufficient to define a protein's three-dimensional structure. In addition, these simulations indicate that the degree of chain association is determined by the balance between specific side-chain packing preferences and the entropy reduction associated with side-chain burial in higher-order multimers.

Computer Simulation↗

PubMed1995

Stimulation of B-cell lymphopoiesis by interleukin-7 leads to aggravation of murine leishmaniasis.

The effect of recombinant interleukin-7 (IL-7) on the clinical course of murine leishmaniasis and the development of the accompanying immune response was investigated. Previously, IL-7 has been shown to possess stimulatory capacity for different cell types of the immune and haematopoietic system critically involved in the defence against Leishmania major (L. major), such as macrophages which are activated for the elimination of the parasite by IL-7. In contrast to these in vitro data, the present study indicates that treatment of genetically susceptible BALB/c mice with IL-7 at the onset of the infection leads to enhanced lesion development and a significantly accelerated death of the animals. This was correlated with a 40-fold increased parasite burden in spleens and lymph nodes. While the specific antibody response against L. major was not altered and lymphocytes of IL-7-treated mice produced comparable amounts of the T-helper type-2 (Th2) cytokines IL-4 and IL-10, less interferon-gamma (IFN-gamma) was measurable after antigenic stimulation of lymph node and spleen cells in vitro. One of the major changes appearing by the first week after infection in IL-7-treated mice was the increase of the total cell number in spleen and lymph nodes draining the local infection. Analysis of the cellular composition revealed that the enhanced cellularity was predominantly due to a rise in the B-cell compartment. Since antigen presentation by B cells has been implicated in the development of Th2 cells, the disease-aggravating activity of IL-7 is thought to be primarily due to augmentation of B lymphopoiesis.

Animals↗

PubMed1994

Prediction of the folding pathways and structure of the GCN4 leucine zipper.

A hierarchical approach is described for the prediction of the three-dimensional structure and folding pathway of the GCN4 leucine zipper. Dimer assembly is simulated by Monte Carlo dynamics. The resulting lowest energy structures undergo cooperative rearrangement of their hydrophobic core leading to side-chain fixation. The coarse-grained structures are further refined using a molecular dynamics annealing protocol. This produces full atom models with a backbone root-mean-square deviation from the crystal structure of 0.81 A. Thus, we demonstrate the predictive ability of our approach to yield high resolution structures of small coiled coils from their sequence.

Amino Acid Sequence↗

PubMed1994

Interleukin-10 inhibits antimicrobial activity against Leishmania major in murine macrophages.

The stimulation of macrophages is of importance to the defense against intracellularly replicating microorganisms such as Leishmania. In this study the direct effect of recombinant interleukin-10 (IL-10) on the leishmanicidal effector functions of murine peritoneal or bone marrow derived macrophages was investigated. IL-10 almost completely inhibited the killing of intracellular leishmania at concentrations above 10 ng/ml. This inhibitory effect was independent of the stimulus used as the activation of macrophages by IFN-gamma and IL-7, recently shown to possess macrophage activating properties, were suppressed by IL-10. Kinetic experiments revealed that IL-10 must be present during the process of macrophage activation and that the leishmanicidal effector function of fully activated macrophages was not influenced. Furthermore, in the absence of exogenously added IL-10, the addition of neutralizing antibodies against IL-10 or IL-10-specific antisense phosphorothioate DNA-oligonucleotide led to an enhanced killing of parasites after stimulation with either IFN-gamma or IL-7. In accordance with this, IL-10 mRNA was readily detectable in murine macrophages by PCR with reverse transcribed mRNA. These results indicate that IL-10, which is endogenously produced by macrophages, acts as an autocrine deactivating factor supporting the survival of the parasite.

Animals↗

PubMed1993

Interleukin-7 enhances antimicrobial activity against Leishmania major in murine macrophages.

Recently, it has been shown that interleukin-7 (IL-7) is able to induce secretion of cytokines and tumoricidal activity by human monocytes. This study shows that treatment of murine macrophages infected with Leishmania major with IL-7 without any other stimulus reduced the percentage of infected cells, as well as the parasite burden per cell, in a dose-dependent manner to a limited degree (45% reduction of the number of amastigotes per 100 macrophages). Simultaneous treatment of macrophages with gamma interferon and IL-7 led to nearly complete (> 99%) elimination of amastigotes. Addition of anti-tumor necrosis factor alpha or N omega-monomethyl-L-arginine acetate reversed the leishmanicidal effects of IL-7, and production of nitric oxide was induced in the presence of IL-7.

Animals↗

PubMed1992

Prediction of protein secondary structure by neural networks: encoding short and long range patterns of amino acid packing.

A complex, cascaded neural network designed to predict the secondary structure of globular proteins has been developed. Information about the local buried-unburied pattern and the average tendency of the particular types of amino acids to be buried inside the globule were used. Nonspecific information about long distance contact maps was also employed. These modifications result in a noticeable improvement (3-9%) of prediction accuracy. The best result for the average success ratio for the testing set of nonhomologous proteins was 68.3% (with corresponding Matthews' coefficients, C alpha,beta,coil equal to 0.60, 0.47, 0.43, respectively).

Amino Acid Sequence↗

PubMed1991

Prediction of protein secondary structure by an enhanced neural network.

Computational model of neural network is used for prediction of secondary structure of globular proteins of known sequence. In contrast to earlier works some information about expected tertiary interactions were built in into the neural network. As a result the prediction accuracy was improved by 3% to 5%. Possible applications of this new approach are briefly discussed.

Amino Acid Sequence↗